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The flickering was reduced by it but not eliminated, and it now had a black background flash, not white as it did previously. However, I had to quickly remove it because many items on the page got misaligned... text aligning right instead of left, and not aligning with images... search box and go-arrow re-arranged vertically... etc etc.

After reading your posts, rather than setting up additional pages for testing as a sandbox (which I don't know how to do), by PM I have sent you the ftp login to the site to be able to test a possible solution.

Kenny,
Within a couple of days I'll be leaving for a place where I won't have a computer. I'll stay away for approx. 2 weeks. In the meantime, John may come up with a good solution for your problem.
I may have found a provisional solution for now. Just put in the head of EACH page, immediately after the opening tag (head):

Btw, there is a rather solid method to kill the flicker in all browsers, but I didn't mention it because it is a totally different approach to menu inclusion (and I seem to be the only one to use it; I developed it myself). Examples here and here.

Kenny,
Just before going abroad (to a place where I don't have a computer), here's something I made some time ago. I had forgotten I ever made it. It explains how we can do page transitions without any flicker at all. That's an absolute garantee. My pages 1, 2 and 3 correspond with yourpages welcome.php, biography.php etc. The only real disadvantage of the method is that the correct url is not displayed in the browser's address bar. But there's a workaround. The technique is explained on page 1. It uses an iframe, but don't be afraid of iframes, they are not deprecated any more.
Arie.

Thanks. Yes, unless we shoot the bird, it will go on flying across the screen even if we go from one page to another.
We could do the same thing with a video. It will go on playing - even on page change - until we close it. That's because page transition does not happen on the level of the main page, but of the iframed page(s).
Arie.

I have the same problem whereas white screen flickers for a second and sometimes stays a white blank screen. It started after reinstalling Windows 7 64-bit then upgrading to IE9. I am also using hta in frames, which downgrades my applications to IE7. Originally thought is was directly related to using the <base href command after the <HEAD> in frames for local files. But it also happens intermittently when just opening the internet explorer. Microsoft does not perform sufficient testing and different IE browsers don't react the same to the base href command. Yes, Microsoft needs a Network Quality Assurance department that performs regression testing on different browsers and OS, instead of relying on the programmer's OS and browser. As a former NQA tester, most companies don't have software testers because... 1) they don't want to pay additional salaries 2) Programmers don't want their programs to fail QA testing 3) And finally they don't want to delays in the program being deployed. I am considering going back to IE 8, but IE8 has issues with the base href. Microsoft has hundreds of issues, and only concentrates on upgrades and not previous versions. YES, SOMEONE SHOULD BE FIRED. NOT THE PROGRAMMER, BUT THE MANAGEMENT THAT DOES NOT ENFORCE ADEQUATE TESTING.

In certain cases, the white flash is even worse in Google Chrome. I noticed it's often caused by window.onload=do_something. Replacing this with <script>do_something()</script> immediately before the closing body tag often reduces or removes the flash.